diff --git a/DESCRIPTION b/DESCRIPTION index 080dbdd5..3c30d0df 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 1.1.0.9021 +Version: 1.2.0 Date: 2020-05-28 Title: Antimicrobial Resistance Analysis Authors@R: c( diff --git a/NAMESPACE b/NAMESPACE index 2249a670..43f56b96 100755 --- a/NAMESPACE +++ b/NAMESPACE @@ -195,61 +195,6 @@ export(set_mo_source) export(skewness) export(susceptibility) export(theme_rsi) -exportMethods("[.ab") -exportMethods("[.disk") -exportMethods("[.mic") -exportMethods("[.mo") -exportMethods("[<-.ab") -exportMethods("[<-.disk") -exportMethods("[<-.mic") -exportMethods("[<-.mo") -exportMethods("[<-.rsi") -exportMethods("[[.ab") -exportMethods("[[.disk") -exportMethods("[[.mic") -exportMethods("[[.mo") -exportMethods("[[<-.ab") -exportMethods("[[<-.disk") -exportMethods("[[<-.mic") -exportMethods("[[<-.mo") -exportMethods("[[<-.rsi") -exportMethods(as.data.frame.ab) -exportMethods(as.data.frame.mo) -exportMethods(as.double.mic) -exportMethods(as.integer.mic) -exportMethods(as.numeric.mic) -exportMethods(barplot.mic) -exportMethods(barplot.rsi) -exportMethods(c.ab) -exportMethods(c.disk) -exportMethods(c.mic) -exportMethods(c.mo) -exportMethods(c.rsi) -exportMethods(droplevels.mic) -exportMethods(droplevels.rsi) -exportMethods(format.bug_drug_combinations) -exportMethods(kurtosis) -exportMethods(kurtosis.data.frame) -exportMethods(kurtosis.default) -exportMethods(kurtosis.matrix) -exportMethods(plot.mic) -exportMethods(plot.rsi) -exportMethods(print.ab) -exportMethods(print.bug_drug_combinations) -exportMethods(print.catalogue_of_life_version) -exportMethods(print.disk) -exportMethods(print.mic) -exportMethods(print.mo) -exportMethods(print.mo_renamed) -exportMethods(print.mo_uncertainties) -exportMethods(print.rsi) -exportMethods(skewness) -exportMethods(skewness.data.frame) -exportMethods(skewness.default) -exportMethods(skewness.matrix) -exportMethods(summary.mic) -exportMethods(summary.mo) -exportMethods(summary.rsi) importFrom(graphics,arrows) importFrom(graphics,axis) importFrom(graphics,barplot) diff --git a/NEWS.md b/NEWS.md index adcd3e51..ebf649cc 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,5 @@ -# AMR 1.1.0.9021 -## Last updated: 28-May-2020 +# AMR 1.2.0 + ### Breaking * Removed code dependency on all other R packages, making this package fully independent of the development process of others. This is a major code change, but will probably not be noticeable by most users. diff --git a/R/ab.R b/R/ab.R index ebdbab09..6c7ca3eb 100755 --- a/R/ab.R +++ b/R/ab.R @@ -343,7 +343,7 @@ is.ab <- function(x) { inherits(x, "ab") } -#' @exportMethod print.ab +#' @method print ab #' @export #' @noRd print.ab <- function(x, ...) { @@ -351,7 +351,7 @@ print.ab <- function(x, ...) { print(as.character(x), quote = FALSE) } -#' @exportMethod as.data.frame.ab +#' @method as.data.frame ab #' @export #' @noRd as.data.frame.ab <- function(x, ...) { @@ -362,7 +362,7 @@ as.data.frame.ab <- function(x, ...) { as.data.frame.vector(as.ab(x), ...) } } -#' @exportMethod [.ab +#' @method [ ab #' @export #' @noRd "[.ab" <- function(x, ...) { @@ -370,7 +370,7 @@ as.data.frame.ab <- function(x, ...) { attributes(y) <- attributes(x) y } -#' @exportMethod [[.ab +#' @method [[ ab #' @export #' @noRd "[[.ab" <- function(x, ...) { @@ -378,7 +378,7 @@ as.data.frame.ab <- function(x, ...) { attributes(y) <- attributes(x) y } -#' @exportMethod [<-.ab +#' @method [<- ab #' @export #' @noRd "[<-.ab" <- function(i, j, ..., value) { @@ -386,7 +386,7 @@ as.data.frame.ab <- function(x, ...) { attributes(y) <- attributes(i) class_integrity_check(y, "antimicrobial code", antibiotics$ab) } -#' @exportMethod [[<-.ab +#' @method [[<- ab #' @export #' @noRd "[[<-.ab" <- function(i, j, ..., value) { @@ -394,7 +394,7 @@ as.data.frame.ab <- function(x, ...) { attributes(y) <- attributes(i) class_integrity_check(y, "antimicrobial code", antibiotics$ab) } -#' @exportMethod c.ab +#' @method c ab #' @export #' @noRd c.ab <- function(x, ...) { diff --git a/R/bug_drug_combinations.R b/R/bug_drug_combinations.R index 3e2405d9..da731829 100644 --- a/R/bug_drug_combinations.R +++ b/R/bug_drug_combinations.R @@ -107,7 +107,7 @@ bug_drug_combinations <- function(x, structure(.Data = out, class = c("bug_drug_combinations", class(x))) } -#' @exportMethod format.bug_drug_combinations +#' @method format bug_drug_combinations #' @export #' @rdname bug_drug_combinations format.bug_drug_combinations <- function(x, @@ -218,7 +218,7 @@ format.bug_drug_combinations <- function(x, y } -#' @exportMethod print.bug_drug_combinations +#' @method print bug_drug_combinations #' @export print.bug_drug_combinations <- function(x, ...) { print(as.data.frame(x, stringsAsFactors = FALSE)) diff --git a/R/catalogue_of_life.R b/R/catalogue_of_life.R index d8938766..9fc0b5bb 100755 --- a/R/catalogue_of_life.R +++ b/R/catalogue_of_life.R @@ -107,7 +107,7 @@ catalogue_of_life_version <- function() { class = c("catalogue_of_life_version", "list")) } -#' @exportMethod print.catalogue_of_life_version +#' @method print catalogue_of_life_version #' @export #' @noRd print.catalogue_of_life_version <- function(x, ...) { diff --git a/R/disk.R b/R/disk.R index 96ac06f1..b8b403cb 100644 --- a/R/disk.R +++ b/R/disk.R @@ -95,7 +95,7 @@ is.disk <- function(x) { inherits(x, "disk") } -#' @exportMethod print.disk +#' @method print disk #' @export #' @noRd print.disk <- function(x, ...) { @@ -103,7 +103,7 @@ print.disk <- function(x, ...) { print(as.integer(x), quote = FALSE) } -#' @exportMethod [.disk +#' @method [ disk #' @export #' @noRd "[.disk" <- function(x, ...) { @@ -111,7 +111,7 @@ print.disk <- function(x, ...) { attributes(y) <- attributes(x) y } -#' @exportMethod [[.disk +#' @method [[ disk #' @export #' @noRd "[[.disk" <- function(x, ...) { @@ -119,7 +119,7 @@ print.disk <- function(x, ...) { attributes(y) <- attributes(x) y } -#' @exportMethod [<-.disk +#' @method [<- disk #' @export #' @noRd "[<-.disk" <- function(i, j, ..., value) { @@ -128,7 +128,7 @@ print.disk <- function(x, ...) { attributes(y) <- attributes(i) y } -#' @exportMethod [[<-.disk +#' @method [[<- disk #' @export #' @noRd "[[<-.disk" <- function(i, j, ..., value) { @@ -137,7 +137,7 @@ print.disk <- function(x, ...) { attributes(y) <- attributes(i) y } -#' @exportMethod c.disk +#' @method c disk #' @export #' @noRd c.disk <- function(x, ...) { diff --git a/R/kurtosis.R b/R/kurtosis.R index f2b019c9..40c2c16d 100755 --- a/R/kurtosis.R +++ b/R/kurtosis.R @@ -25,7 +25,6 @@ #' @inheritSection lifecycle Questioning lifecycle #' @param x a vector of values, a [`matrix`] or a [`data.frame`] #' @param na.rm a logical value indicating whether `NA` values should be stripped before the computation proceeds. -#' @exportMethod kurtosis #' @seealso [skewness()] #' @rdname kurtosis #' @inheritSection AMR Read more on our website! @@ -34,7 +33,7 @@ kurtosis <- function(x, na.rm = FALSE) { UseMethod("kurtosis") } -#' @exportMethod kurtosis.default +#' @method kurtosis default #' @rdname kurtosis #' @export kurtosis.default <- function(x, na.rm = FALSE) { @@ -47,14 +46,14 @@ kurtosis.default <- function(x, na.rm = FALSE) { (base::sum((x - base::mean(x, na.rm = na.rm))^2, na.rm = na.rm)^2) } -#' @exportMethod kurtosis.matrix +#' @method kurtosis matrix #' @rdname kurtosis #' @export kurtosis.matrix <- function(x, na.rm = FALSE) { base::apply(x, 2, kurtosis.default, na.rm = na.rm) } -#' @exportMethod kurtosis.data.frame +#' @method kurtosis data.frame #' @rdname kurtosis #' @export kurtosis.data.frame <- function(x, na.rm = FALSE) { diff --git a/R/mic.R b/R/mic.R index 8f7cdb03..1715b87d 100755 --- a/R/mic.R +++ b/R/mic.R @@ -140,28 +140,28 @@ is.mic <- function(x) { inherits(x, "mic") } -#' @exportMethod as.double.mic +#' @method as.double mic #' @export #' @noRd as.double.mic <- function(x, ...) { as.double(gsub("(<|=|>)+", "", as.character(x))) } -#' @exportMethod as.integer.mic +#' @method as.integer mic #' @export #' @noRd as.integer.mic <- function(x, ...) { as.integer(gsub("(<|=|>)+", "", as.character(x))) } -#' @exportMethod as.numeric.mic +#' @method as.numeric mic #' @export #' @noRd as.numeric.mic <- function(x, ...) { as.numeric(gsub("(<|=|>)+", "", as.character(x))) } -#' @exportMethod droplevels.mic +#' @method droplevels mic #' @export #' @noRd droplevels.mic <- function(x, exclude = ifelse(anyNA(levels(x)), NULL, NA), ...) { @@ -170,7 +170,7 @@ droplevels.mic <- function(x, exclude = ifelse(anyNA(levels(x)), NULL, NA), ...) x } -#' @exportMethod print.mic +#' @method print mic #' @export #' @noRd print.mic <- function(x, ...) { @@ -178,7 +178,7 @@ print.mic <- function(x, ...) { print(as.character(x), quote = FALSE) } -#' @exportMethod summary.mic +#' @method summary mic #' @export #' @noRd summary.mic <- function(object, ...) { @@ -194,7 +194,7 @@ summary.mic <- function(object, ...) { ) } -#' @exportMethod plot.mic +#' @method plot mic #' @export #' @importFrom graphics barplot axis par #' @noRd @@ -213,7 +213,7 @@ plot.mic <- function(x, axis(2, seq(0, max(table(droplevels.factor(x))))) } -#' @exportMethod barplot.mic +#' @method barplot mic #' @export #' @importFrom graphics barplot axis #' @noRd @@ -232,7 +232,7 @@ barplot.mic <- function(height, axis(2, seq(0, max(table(droplevels.factor(height))))) } -#' @exportMethod [.mic +#' @method [ mic #' @export #' @noRd "[.mic" <- function(x, ...) { @@ -240,7 +240,7 @@ barplot.mic <- function(height, attributes(y) <- attributes(x) y } -#' @exportMethod [[.mic +#' @method [[ mic #' @export #' @noRd "[[.mic" <- function(x, ...) { @@ -248,7 +248,7 @@ barplot.mic <- function(height, attributes(y) <- attributes(x) y } -#' @exportMethod [<-.mic +#' @method [<- mic #' @export #' @noRd "[<-.mic" <- function(i, j, ..., value) { @@ -257,7 +257,7 @@ barplot.mic <- function(height, attributes(y) <- attributes(i) y } -#' @exportMethod [[<-.mic +#' @method [[<- mic #' @export #' @noRd "[[<-.mic" <- function(i, j, ..., value) { @@ -266,7 +266,7 @@ barplot.mic <- function(height, attributes(y) <- attributes(i) y } -#' @exportMethod c.mic +#' @method c mic #' @export #' @noRd c.mic <- function(x, ...) { diff --git a/R/mo.R b/R/mo.R index 9d2270ad..fc6594bf 100755 --- a/R/mo.R +++ b/R/mo.R @@ -1566,7 +1566,7 @@ format_uncertainty_as_df <- function(uncertainty_level, df } -#' @exportMethod print.mo +#' @method print mo #' @export #' @noRd print.mo <- function(x, ...) { @@ -1577,7 +1577,7 @@ print.mo <- function(x, ...) { print.default(x, quote = FALSE) } -#' @exportMethod summary.mo +#' @method summary mo #' @export #' @noRd summary.mo <- function(object, ...) { @@ -1593,7 +1593,7 @@ summary.mo <- function(object, ...) { "#3" = top_3[3]) } -#' @exportMethod as.data.frame.mo +#' @method as.data.frame mo #' @export #' @noRd as.data.frame.mo <- function(x, ...) { @@ -1605,7 +1605,7 @@ as.data.frame.mo <- function(x, ...) { } } -#' @exportMethod [.mo +#' @method [ mo #' @export #' @noRd "[.mo" <- function(x, ...) { @@ -1613,7 +1613,7 @@ as.data.frame.mo <- function(x, ...) { attributes(y) <- attributes(x) y } -#' @exportMethod [[.mo +#' @method [[ mo #' @export #' @noRd "[[.mo" <- function(x, ...) { @@ -1621,7 +1621,7 @@ as.data.frame.mo <- function(x, ...) { attributes(y) <- attributes(x) y } -#' @exportMethod [<-.mo +#' @method [<- mo #' @export #' @noRd "[<-.mo" <- function(i, j, ..., value) { @@ -1631,7 +1631,7 @@ as.data.frame.mo <- function(x, ...) { class_integrity_check(y, "microorganism code", c(as.character(microorganisms$mo), as.character(microorganisms.translation$mo_old))) } -#' @exportMethod [[<-.mo +#' @method [[<- mo #' @export #' @noRd "[[<-.mo" <- function(i, j, ..., value) { @@ -1641,7 +1641,7 @@ as.data.frame.mo <- function(x, ...) { class_integrity_check(y, "microorganism code", c(as.character(microorganisms$mo), as.character(microorganisms.translation$mo_old))) } -#' @exportMethod c.mo +#' @method c mo #' @export #' @noRd c.mo <- function(x, ...) { @@ -1668,7 +1668,7 @@ mo_uncertainties <- function() { class = c("mo_uncertainties", "data.frame")) } -#' @exportMethod print.mo_uncertainties +#' @method print mo_uncertainties #' @export #' @noRd print.mo_uncertainties <- function(x, ...) { @@ -1717,7 +1717,7 @@ mo_renamed <- function() { class = c("mo_renamed", "data.frame")) } -#' @exportMethod print.mo_renamed +#' @method print mo_renamed #' @export #' @noRd print.mo_renamed <- function(x, ...) { diff --git a/R/resistance_predict.R b/R/resistance_predict.R index 5d77df5a..d121836a 100755 --- a/R/resistance_predict.R +++ b/R/resistance_predict.R @@ -302,7 +302,7 @@ resistance_predict <- function(x, #' @export rsi_predict <- resistance_predict -#' @exportMethod plot.mic +#' @method plot resistance_predict #' @export #' @importFrom graphics axis arrows points #' @rdname resistance_predict diff --git a/R/rsi.R b/R/rsi.R index 9d16b432..35cd711a 100755 --- a/R/rsi.R +++ b/R/rsi.R @@ -529,7 +529,7 @@ is.rsi.eligible <- function(x, threshold = 0.05) { } } -#' @exportMethod print.rsi +#' @method print rsi #' @export #' @noRd print.rsi <- function(x, ...) { @@ -537,7 +537,7 @@ print.rsi <- function(x, ...) { print(as.character(x), quote = FALSE) } -#' @exportMethod droplevels.rsi +#' @method droplevels rsi #' @export #' @noRd droplevels.rsi <- function(x, exclude = if (anyNA(levels(x))) NULL else NA, ...) { @@ -546,7 +546,7 @@ droplevels.rsi <- function(x, exclude = if (anyNA(levels(x))) NULL else NA, ...) x } -#' @exportMethod summary.rsi +#' @method summary rsi #' @export #' @noRd summary.rsi <- function(object, ...) { @@ -561,7 +561,7 @@ summary.rsi <- function(object, ...) { ) } -#' @exportMethod plot.rsi +#' @method plot rsi #' @export #' @importFrom graphics text axis #' @noRd @@ -618,7 +618,7 @@ plot.rsi <- function(x, } -#' @exportMethod barplot.rsi +#' @method barplot rsi #' @export #' @importFrom graphics barplot axis par #' @noRd @@ -652,7 +652,7 @@ barplot.rsi <- function(height, } } -#' @exportMethod [<-.rsi +#' @method [<- rsi #' @export #' @noRd "[<-.rsi" <- function(i, j, ..., value) { @@ -661,7 +661,7 @@ barplot.rsi <- function(height, attributes(y) <- attributes(i) y } -#' @exportMethod [[<-.rsi +#' @method [[<- rsi #' @export #' @noRd "[[<-.rsi" <- function(i, j, ..., value) { @@ -670,7 +670,7 @@ barplot.rsi <- function(height, attributes(y) <- attributes(i) y } -#' @exportMethod c.rsi +#' @method c rsi #' @export #' @noRd c.rsi <- function(x, ...) { diff --git a/R/skewness.R b/R/skewness.R index 35d2458f..455de80c 100755 --- a/R/skewness.R +++ b/R/skewness.R @@ -27,7 +27,6 @@ #' @inheritSection lifecycle Questioning lifecycle #' @param x a vector of values, a [`matrix`] or a [`data.frame`] #' @param na.rm a logical value indicating whether `NA` values should be stripped before the computation proceeds. -#' @exportMethod skewness #' @seealso [kurtosis()] #' @rdname skewness #' @inheritSection AMR Read more on our website! @@ -36,7 +35,7 @@ skewness <- function(x, na.rm = FALSE) { UseMethod("skewness") } -#' @exportMethod skewness.default +#' @method skewness default #' @rdname skewness #' @export skewness.default <- function(x, na.rm = FALSE) { @@ -48,14 +47,14 @@ skewness.default <- function(x, na.rm = FALSE) { (base::sum((x - base::mean(x))^3) / n) / (base::sum((x - base::mean(x)) ^ 2) / n) ^ (3 / 2) } -#' @exportMethod skewness.matrix +#' @method skewness matrix #' @rdname skewness #' @export skewness.matrix <- function(x, na.rm = FALSE) { base::apply(x, 2, skewness.default, na.rm = na.rm) } -#' @exportMethod skewness.data.frame +#' @method skewness data.frame #' @rdname skewness #' @export skewness.data.frame <- function(x, na.rm = FALSE) { diff --git a/cran-comments.md b/cran-comments.md index d5de3b05..5652aa72 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,5 +1,3 @@ -* Although the previous release (1.0.1) is from 2020-02-23, this updates provides support for the upcoming dplyr 1.0.0 which is used (and relied upon) by probably all our users. - -* For this specific version, otherwise nothing to mention. +* For this specific version, nothing to mention. * Since version 0.3.0, CHECK returns a NOTE for having a data directory over 3 MB. This is needed to offer users reference data for the complete taxonomy of microorganisms - one of the most important features of this package. diff --git a/docs/404.html b/docs/404.html index 40d22457..528cd0c4 100644 --- a/docs/404.html +++ b/docs/404.html @@ -81,7 +81,7 @@ AMR (for R) - 1.1.0.9021 + 1.2.0 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index 070e9fa7..351386e6 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -81,7 +81,7 @@ AMR (for R) - 1.1.0.9021 + 1.2.0 diff --git a/docs/articles/AMR.html b/docs/articles/AMR.html index fd671271..7fbe2425 100644 --- a/docs/articles/AMR.html +++ b/docs/articles/AMR.html @@ -39,7 +39,7 @@ AMR (for R) - 1.1.0.9021 + 1.2.0 @@ -336,54 +336,32 @@ -2015-07-23 -Z5 -Hospital B -Streptococcus pneumoniae -S -S -S -S -F - - -2017-01-21 -D6 -Hospital C -Staphylococcus aureus -S -S -S -S -M - - -2014-05-20 -Y10 +2013-12-18 +P10 Hospital A Escherichia coli +R S -I S S F -2017-11-02 -M10 -Hospital D -Staphylococcus aureus +2010-07-10 +K6 +Hospital C +Escherichia coli +S S S -R S M -2014-08-26 -B4 +2014-12-14 +F6 Hospital C -Staphylococcus aureus +Escherichia coli S S S @@ -391,11 +369,33 @@ M -2013-05-29 -R3 +2010-12-31 +N8 +Hospital D +Escherichia coli +S +S +S +S +F + + +2010-11-24 +M5 Hospital B Escherichia coli S +S +S +S +M + + +2010-10-07 +Z8 +Hospital C +Escherichia coli +R R S S @@ -432,16 +432,16 @@ Longest: 1

1 M -10,518 -52.59% -10,518 -52.59% +10,397 +51.99% +10,397 +51.99% 2 F -9,482 -47.41% +9,603 +48.02% 20,000 100.00% @@ -491,7 +491,7 @@ Longest: 1

First weighted isolates

-

We made a slight twist to the CLSI algorithm, to take into account the antimicrobial susceptibility profile. Have a look at all isolates of patient P10, sorted on date:

+

We made a slight twist to the CLSI algorithm, to take into account the antimicrobial susceptibility profile. Have a look at all isolates of patient U2, sorted on date:

@@ -507,10 +507,10 @@ Longest: 1

- - + + - + @@ -518,43 +518,43 @@ Longest: 1

- - + + - - - + + + - - + + + + - - - - + + - - + + - - + + - + @@ -562,62 +562,62 @@ Longest: 1

- - + + + - - - + + - + - - + + + - - + - - + + + - - + - - + + - +
isolate
12010-01-22P102010-03-30U2 B_ESCHR_COLIIR S S S
22010-02-24P102010-07-30U2 B_ESCHR_COLISSS RSSS FALSE
32010-03-10P102010-10-14U2 B_ESCHR_COLIRS S SRR FALSE
42010-03-25P102010-12-17U2 B_ESCHR_COLIR S SRSS FALSE
52010-04-30P102011-02-17U2 B_ESCHR_COLISR S S S
62010-05-05P102011-03-17U2 B_ESCHR_COLII S SR S FALSE
72010-05-19P102011-06-10U2 B_ESCHR_COLI R S S SFALSETRUE
82010-05-27P102011-07-17U2 B_ESCHR_COLIR S SSSR FALSE
92010-10-01P102011-08-08U2 B_ESCHR_COLII SSSR S FALSE
102010-11-19P102011-08-21U2 B_ESCHR_COLI SR SR S FALSE
-

Only 1 isolates are marked as ‘first’ according to CLSI guideline. But when reviewing the antibiogram, it is obvious that some isolates are absolutely different strains and should be included too. This is why we weigh isolates, based on their antibiogram. The key_antibiotics() function adds a vector with 18 key antibiotics: 6 broad spectrum ones, 6 small spectrum for Gram negatives and 6 small spectrum for Gram positives. These can be defined by the user.

+

Only 2 isolates are marked as ‘first’ according to CLSI guideline. But when reviewing the antibiogram, it is obvious that some isolates are absolutely different strains and should be included too. This is why we weigh isolates, based on their antibiogram. The key_antibiotics() function adds a vector with 18 key antibiotics: 6 broad spectrum ones, 6 small spectrum for Gram negatives and 6 small spectrum for Gram positives. These can be defined by the user.

If a column exists with a name like ‘key(…)ab’ the first_isolate() function will automatically use it and determine the first weighted isolates. Mind the NOTEs in below output:

data <- data %>%
   mutate(keyab = key_antibiotics(.)) %>%
@@ -643,10 +643,10 @@ Longest: 1

 
 
 1
-2010-01-22
-P10
+2010-03-30
+U2
 B_ESCHR_COLI
-I
+R
 S
 S
 S
@@ -655,46 +655,46 @@ Longest: 1

 
 
 2
-2010-02-24
-P10
+2010-07-30
+U2
 B_ESCHR_COLI
-S
-S
-S
 R
+S
+S
+S
+FALSE
 FALSE
-TRUE
 
 
 3
-2010-03-10
-P10
+2010-10-14
+U2
 B_ESCHR_COLI
+R
+S
 S
 S
-R
-R
 FALSE
-TRUE
+FALSE
 
 
 4
-2010-03-25
-P10
+2010-12-17
+U2
 B_ESCHR_COLI
-R
 S
 S
-R
+S
+S
 FALSE
 TRUE
 
 
 5
-2010-04-30
-P10
+2011-02-17
+U2
 B_ESCHR_COLI
-S
+R
 S
 S
 S
@@ -703,71 +703,71 @@ Longest: 1

 
 
 6
-2010-05-05
-P10
+2011-03-17
+U2
 B_ESCHR_COLI
+I
 S
 S
-R
 S
 FALSE
-TRUE
+FALSE
 
 
 7
-2010-05-19
-P10
+2011-06-10
+U2
 B_ESCHR_COLI
 R
 S
 S
 S
-FALSE
+TRUE
 TRUE
 
 
 8
-2010-05-27
-P10
+2011-07-17
+U2
 B_ESCHR_COLI
+R
 S
 S
-S
-S
+R
 FALSE
 TRUE
 
 
 9
-2010-10-01
-P10
-B_ESCHR_COLI
-S
-S
-S
-S
-FALSE
-FALSE
-
-
-10
-2010-11-19
-P10
+2011-08-08
+U2
 B_ESCHR_COLI
+I
 S
 R
 S
-S
 FALSE
 TRUE
 
+
+10
+2011-08-21
+U2
+B_ESCHR_COLI
+S
+S
+R
+S
+FALSE
+FALSE
+
 
 
-
Instead of 1, now 9 isolates are flagged. In total, 78.3% of all isolates are marked ‘first weighted’ - 49.8% more than when using the CLSI guideline. In real life, this novel algorithm will yield 5-10% more isolates than the classic CLSI guideline.

+
Instead of 2, now 6 isolates are flagged. In total, 78.7% of all isolates are marked ‘first weighted’ - 50.2% more than when using the CLSI guideline. In real life, this novel algorithm will yield 5-10% more isolates than the classic CLSI guideline.

 
As with filter_first_isolate(), there’s a shortcut for this new algorithm too:

 
data_1st <- data %>%
   filter_first_weighted_isolate()

-
So we end up with 15,654 isolates for analysis.

+
So we end up with 15,741 isolates for analysis.

 
We can remove unneeded columns:

 
data_1st <- data_1st %>%
   select(-c(first, keyab))

@@ -775,7 +775,6 @@ Longest: 1

 
head(data_1st)

 
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data_1st %>% freq(genus, species)
Frequency table
Class: character

-Length: 15,654

-Available: 15,654 (100%, NA: 0 = 0%)

+Length: 15,741

+Available: 15,741 (100%, NA: 0 = 0%)

 Unique: 4
Shortest: 16

 Longest: 24

@@ -924,33 +917,33 @@ Longest: 24

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The functions resistance() and susceptibility() can be used to calculate antimicrobial resistance or susceptibility. For more specific analyses, the functions proportion_S(), proportion_SI(), proportion_I(), proportion_IR() and proportion_R() can be used to determine the proportion of a specific antimicrobial outcome.
As per the EUCAST guideline of 2019, we calculate resistance as the proportion of R (proportion_R(), equal to resistance()) and susceptibility as the proportion of S and I (proportion_SI(), equal to susceptibility()). These functions can be used on their own:
data_1st %>% resistance(AMX)
-# [1] 0.4435288

+# [1] 0.4476209
Or can be used in conjuction with group_by() and summarise(), both from the dplyr package:
data_1st %>%
   group_by(hospital) %>%
@@ -975,19 +968,19 @@ Longest: 24

 

-
+
-
+
-
+
-
+

 

 date
 patient_id
 hospital
 

 
 
12015-07-23Z5Hospital BB_STRPT_PNMNSSSRFGram-positiveStreptococcuspneumoniaeTRUE
22017-01-21D6Hospital CB_STPHY_AURSSSSSMGram-positiveStaphylococcusaureusTRUE
42017-11-02M10Hospital DB_STPHY_AURSSSRSMGram-positiveStaphylococcusaureusTRUE
52014-08-26B4Hospital CB_STPHY_AURSSSSSMGram-positiveStaphylococcusaureusTRUE
62013-05-29R3Hospital B2013-12-18P10Hospital A
 B_ESCHR_COLIS
 R
 S
 SS
 F
 Gram-negative
 Escherichia
 TRUE
 

 
72013-12-10T32010-07-10K6Hospital CB_ESCHR_COLISSSSMGram-negativeEscherichiacoliTRUE
2014-12-14F6Hospital CB_ESCHR_COLISSSSMGram-negativeEscherichiacoliTRUE
2010-12-31N8Hospital DB_ESCHR_COLISSSSFGram-negativeEscherichiacoliTRUE
2010-11-24M5
 Hospital B
 B_ESCHR_COLI
 S
 S
 S
 SMGram-negativeEscherichiacoliTRUE
2010-10-07Z8Hospital CB_ESCHR_COLIRRSS
 F
 Gram-negative
 Escherichia
 
 
 
 
 

 1
 Escherichia coli7,77849.69%7,77849.69%7,94350.46%7,94350.46%
 

 

 2
 Staphylococcus aureus3,99925.55%11,77775.23%3,97825.27%11,92175.73%
 

 

 3
 Streptococcus pneumoniae2,30014.69%14,07789.93%2,24814.28%14,16990.01%
 

 

 4
 Klebsiella pneumoniae1,57710.07%15,6541,5729.99%15,741
 100.00%
 

 
 
 
 
 
 
 

 Hospital A0.44612390.4402730
 

 

 Hospital B0.44047620.4607609
 

 

 Hospital C0.45497630.4437526
 

 

 Hospital D0.43666880.4389635
 

 
 

@@ -1005,23 +998,23 @@ Longest: 24

 
 
 Hospital A
-0.4461239
-4631
+0.4402730
+4688
 
 
 Hospital B
-0.4404762
-5544
+0.4607609
+5441
 
 
 Hospital C
-0.4549763
-2321
+0.4437526
+2409
 
 
 Hospital D
-0.4366688
-3158
+0.4389635
+3203
 
 
 
@@ -1041,27 +1034,27 @@ Longest: 24

 
 
 Escherichia
-0.8215480
-0.8976601
-0.9835433
+0.8296613
+0.8992824
+0.9862772
 
 
 Klebsiella
-0.8300571
-0.8972733
-0.9866836
+0.8250636
+0.9083969
+0.9840967
 
 
 Staphylococcus
-0.8202051
-0.9229807
-0.9832458
+0.8245349
+0.9263449
+0.9891905
 
 
 Streptococcus
-0.6204348
+0.6107651
 0.0000000
-0.6204348
+0.6107651
 
 
 
diff --git a/docs/articles/AMR_files/figure-html/plot 1-1.png b/docs/articles/AMR_files/figure-html/plot 1-1.png
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index 958d0f1a..1e18c8ff 100644
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diff --git a/docs/articles/EUCAST.html b/docs/articles/EUCAST.html
index 4f787ab1..42fb770f 100644
--- a/docs/articles/EUCAST.html
+++ b/docs/articles/EUCAST.html
@@ -39,7 +39,7 @@
       
       
         AMR (for R)
-        1.1.0.9016
+        1.2.0
@@ -186,7 +186,7 @@

How to apply EUCAST rules

Matthijs S. Berends

-

21 May 2020

+

28 May 2020

Source: vignettes/EUCAST.Rmd @@ -301,6 +301,8 @@ 
eucast_rules(data)
+
# Warning: Not all columns with antimicrobial results are of class <rsi>.
+# Transform eligible columns to class <rsi> on beforehand: your_data %>% mutate_if(is.rsi.eligible, as.rsi)
diff --git a/docs/articles/MDR.html b/docs/articles/MDR.html index cc06cb1f..f5b31017 100644 --- a/docs/articles/MDR.html +++ b/docs/articles/MDR.html @@ -39,7 +39,7 @@ AMR (for R) - 1.1.0.9021 + 1.2.0 @@ -302,19 +302,19 @@ Unique: 2

The data set now looks like this:

head(my_TB_data)
 #   rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin
-# 1          R         S            R          I            I            S
-# 2          S         R            S          I            R            I
-# 3          S         S            I          S            R            R
-# 4          I         R            S          S            I            S
-# 5          S         S            R          R            R            S
-# 6          I         R            R          R            R            S
+# 1          S         R            R          S            R            R
+# 2          R         S            R          S            R            S
+# 3          R         R            S          S            R            S
+# 4          S         S            S          S            R            S
+# 5          S         R            S          S            R            S
+# 6          R         S            R          S            S            S
 #   kanamycin
 # 1         R
-# 2         S
-# 3         I
+# 2         I
+# 3         R
 # 4         S
 # 5         R
-# 6         I
+# 6 S

We can now add the interpretation of MDR-TB to our data set. You can use:

mdro(my_TB_data, guideline = "TB")

or its shortcut mdr_tb():

@@ -343,40 +343,40 @@ Unique: 5

- - - - + + + + - - - - + + + + - - - - + + + + - - - - + + + + - - + + diff --git a/docs/articles/PCA.html b/docs/articles/PCA.html index e65fca7d..6694bba8 100644 --- a/docs/articles/PCA.html +++ b/docs/articles/PCA.html @@ -39,7 +39,7 @@ AMR (for R) - 1.1.0.9021 + 1.2.0 diff --git a/docs/articles/SPSS.html b/docs/articles/SPSS.html index 87da5d0c..11cde0ec 100644 --- a/docs/articles/SPSS.html +++ b/docs/articles/SPSS.html @@ -39,7 +39,7 @@ AMR (for R) - 1.1.0 + 1.2.0 @@ -186,7 +186,7 @@

How to import data from SPSS / SAS / Stata

Matthijs S. Berends

-

15 April 2020

+

28 May 2020

Source: vignettes/SPSS.Rmd @@ -242,10 +242,10 @@

To demonstrate the first point:

# not all values are valid MIC values:
 as.mic(0.125)
-# Class 'mic'
+# Class <mic>
 # [1] 0.125
 as.mic("testvalue")
-# Class 'mic'
+# Class <mic>
 # [1] <NA>
 
 # the Gram stain is avaiable for all bacteria:
@@ -398,7 +398,7 @@
-

Site built with pkgdown 1.5.0.

+

Site built with pkgdown 1.5.1.

diff --git a/docs/articles/WHONET.html b/docs/articles/WHONET.html index ce6c2ad4..15652aaf 100644 --- a/docs/articles/WHONET.html +++ b/docs/articles/WHONET.html @@ -39,7 +39,7 @@ AMR (for R) - 1.1.0.9015 + 1.2.0 @@ -186,7 +186,7 @@

How to work with WHONET data

Matthijs S. Berends

-

20 May 2020

+

28 May 2020

Source: vignettes/WHONET.Rmd @@ -232,7 +232,7 @@

Class: character
Length: 500
Available: 500 (100%, NA: 0 = 0%)
-Unique: 39

+Unique: 37

Shortest: 11
Longest: 40

mo
1 Mono-resistant319263.84%319263.84%324564.90%324564.90%
2 Negative66713.34%385977.18%67813.56%392378.46%
3 Multi-drug-resistant63712.74%449689.92%60712.14%453090.60%
4 Poly-resistant2875.74%478395.66%2625.24%479295.84%
5 Extensively drug-resistant2174.34%2084.16% 5000 100.00%
@@ -319,15 +319,15 @@ Longest: 40

- - - - - + + + + +
10Enterococcus columbae40.8%44388.6%Streptococcus anginosus51.0%44488.8%
-

(omitted 29 entries, n = 57 [11.40%])

+

(omitted 27 entries, n = 56 [11.20%])

# our transformed antibiotic columns
 # amoxicillin/clavulanic acid (J01CR02) as an example
 data %>% freq(AMC_ND2)
diff --git a/docs/articles/benchmarks.html b/docs/articles/benchmarks.html index 6485137b..e86204ed 100644 --- a/docs/articles/benchmarks.html +++ b/docs/articles/benchmarks.html @@ -39,7 +39,7 @@ AMR (for R) - 1.1.0.9021 + 1.2.0
@@ -221,21 +221,21 @@ times = 10) print(S.aureus, unit = "ms", signif = 2) # Unit: milliseconds -# expr min lq mean median uq max -# as.mo("sau") 8.2 9.7 22.0 14.0 38.0 43 -# as.mo("stau") 130.0 130.0 160.0 170.0 170.0 190 -# as.mo("STAU") 120.0 130.0 150.0 150.0 180.0 190 -# as.mo("staaur") 8.3 9.1 13.0 9.4 10.0 40 -# as.mo("STAAUR") 8.0 9.3 15.0 10.0 13.0 35 -# as.mo("S. aureus") 9.3 11.0 26.0 14.0 15.0 120 -# as.mo("S aureus") 10.0 12.0 22.0 13.0 38.0 49 -# as.mo("Staphylococcus aureus") 6.6 7.7 8.5 8.6 9.1 10 -# as.mo("Staphylococcus aureus (MRSA)") 820.0 860.0 890.0 880.0 930.0 1000 -# as.mo("Sthafilokkockus aaureuz") 350.0 350.0 370.0 370.0 370.0 380 -# as.mo("MRSA") 7.8 9.1 13.0 10.0 11.0 42 -# as.mo("VISA") 11.0 12.0 19.0 13.0 15.0 47 -# as.mo("VRSA") 11.0 12.0 21.0 14.0 39.0 42 -# as.mo(22242419) 130.0 140.0 150.0 140.0 150.0 190 +# expr min lq mean median uq max +# as.mo("sau") 8.5 11.0 17.0 12.0 12.0 43.0 +# as.mo("stau") 120.0 130.0 150.0 140.0 160.0 180.0 +# as.mo("STAU") 130.0 140.0 150.0 150.0 160.0 170.0 +# as.mo("staaur") 7.7 9.1 13.0 11.0 12.0 38.0 +# as.mo("STAAUR") 8.3 9.3 15.0 10.0 11.0 37.0 +# as.mo("S. aureus") 11.0 12.0 18.0 13.0 14.0 41.0 +# as.mo("S aureus") 8.8 11.0 17.0 12.0 13.0 41.0 +# as.mo("Staphylococcus aureus") 6.4 6.6 7.4 7.6 7.8 9.1 +# as.mo("Staphylococcus aureus (MRSA)") 810.0 870.0 890.0 890.0 900.0 1000.0 +# as.mo("Sthafilokkockus aaureuz") 320.0 340.0 370.0 350.0 400.0 490.0 +# as.mo("MRSA") 9.2 10.0 13.0 11.0 12.0 37.0 +# as.mo("VISA") 12.0 12.0 22.0 13.0 43.0 44.0 +# as.mo("VRSA") 11.0 13.0 21.0 14.0 38.0 41.0 +# as.mo(22242419) 130.0 140.0 150.0 140.0 170.0 200.0 # neval # 10 # 10 @@ -262,12 +262,12 @@ times = 10) print(M.semesiae, unit = "ms", signif = 4) # Unit: milliseconds -# expr min lq mean median uq max -# as.mo("metsem") 135.600 143.500 157.800 153.400 175.70 191.40 -# as.mo("METSEM") 139.700 140.800 158.100 148.300 176.10 188.50 -# as.mo("M. semesiae") 9.010 9.317 13.280 9.802 12.51 40.46 -# as.mo("M. semesiae") 9.155 9.321 9.665 9.557 10.07 10.37 -# as.mo("Methanosarcina semesiae") 6.737 7.160 16.020 8.413 33.21 37.10 +# expr min lq mean median uq max +# as.mo("metsem") 143.400 146.300 156.10 155.400 164.900 176.40 +# as.mo("METSEM") 141.600 146.900 167.00 170.700 185.000 188.00 +# as.mo("M. semesiae") 9.665 9.879 16.50 10.090 11.960 44.29 +# as.mo("M. semesiae") 10.000 10.080 14.46 11.660 13.140 42.01 +# as.mo("Methanosarcina semesiae") 7.161 7.389 10.40 7.542 9.294 33.00 # neval # 10 # 10 @@ -307,7 +307,7 @@ print(run_it, unit = "ms", signif = 3) # Unit: milliseconds # expr min lq mean median uq max neval -# mo_name(x) 1670 1740 1800 1790 1880 1900 10 +# mo_name(x) 1650 1730 1790 1790 1840 1900 10

So transforming 500,000 values (!!) of 50 unique values only takes 1.79 seconds. You only lose time on your unique input values.

@@ -320,10 +320,10 @@ times = 10) print(run_it, unit = "ms", signif = 3) # Unit: milliseconds -# expr min lq mean median uq max neval -# A 5.630 5.900 6.420 6.480 6.910 7.120 10 -# B 9.940 11.300 15.000 11.800 12.300 45.300 10 -# C 0.247 0.277 0.315 0.295 0.358 0.386 10
+# expr min lq mean median uq max neval +# A 5.680 5.820 9.61 6.36 6.850 39.500 10 +# B 9.790 10.000 10.60 10.40 10.900 11.900 10 +# C 0.229 0.259 0.27 0.27 0.286 0.311 10

So going from mo_name("Staphylococcus aureus") to "Staphylococcus aureus" takes 0.0003 seconds - it doesn’t even start calculating if the result would be the same as the expected resulting value. That goes for all helper functions:

run_it <- microbenchmark(A = mo_species("aureus"),
                          B = mo_genus("Staphylococcus"),
@@ -337,14 +337,14 @@
 print(run_it, unit = "ms", signif = 3)
 # Unit: milliseconds
 #  expr   min    lq  mean median    uq   max neval
-#     A 0.207 0.214 0.241  0.218 0.240 0.412    10
-#     B 0.178 0.207 0.215  0.211 0.219 0.272    10
-#     C 0.218 0.221 0.234  0.233 0.240 0.264    10
-#     D 0.203 0.211 0.221  0.214 0.218 0.290    10
-#     E 0.208 0.209 0.223  0.214 0.227 0.279    10
-#     F 0.172 0.203 0.222  0.212 0.222 0.302    10
-#     G 0.200 0.202 0.212  0.208 0.213 0.253    10
-#     H 0.193 0.194 0.208  0.200 0.215 0.261    10
+# A 0.209 0.221 0.236 0.225 0.244 0.311 10 +# B 0.197 0.201 0.215 0.212 0.222 0.266 10 +# C 0.205 0.224 0.243 0.229 0.242 0.383 10 +# D 0.199 0.207 0.216 0.211 0.214 0.270 10 +# E 0.196 0.206 0.218 0.215 0.221 0.270 10 +# F 0.188 0.197 0.212 0.210 0.216 0.269 10 +# G 0.195 0.198 0.213 0.203 0.215 0.299 10 +# H 0.184 0.193 0.205 0.201 0.207 0.252 10

Of course, when running mo_phylum("Firmicutes") the function has zero knowledge about the actual microorganism, namely S. aureus. But since the result would be "Firmicutes" anyway, there is no point in calculating the result. And because this package ‘knows’ all phyla of all known bacteria (according to the Catalogue of Life), it can just return the initial value immediately.

@@ -370,14 +370,14 @@ times = 100) print(run_it, unit = "ms", signif = 4) # Unit: milliseconds -# expr min lq mean median uq max neval -# en 11.24 11.97 16.09 13.31 13.71 48.40 100 -# de 12.18 12.84 19.63 14.33 15.00 55.14 100 -# nl 16.24 17.07 24.36 18.61 19.83 55.70 100 -# es 12.23 12.77 17.38 13.71 14.72 51.57 100 -# it 12.15 13.01 18.55 14.03 14.81 146.90 100 -# fr 12.23 13.08 16.81 14.30 14.86 49.30 100 -# pt 12.30 12.85 18.13 14.24 14.88 49.70 100
+# expr min lq mean median uq max neval +# en 9.303 11.59 14.90 12.40 13.63 45.92 100 +# de 10.080 12.39 15.77 13.11 14.45 46.27 100 +# nl 13.200 16.26 20.88 17.80 19.52 49.93 100 +# es 9.957 12.23 15.57 13.12 14.59 51.99 100 +# it 10.210 12.44 19.02 13.34 14.74 52.96 100 +# fr 10.040 12.40 18.90 13.26 15.07 54.40 100 +# pt 10.450 12.67 16.91 13.46 14.68 51.47 100

Currently supported are German, Dutch, Spanish, Italian, French and Portuguese.

diff --git a/docs/articles/benchmarks_files/figure-html/unnamed-chunk-4-1.png b/docs/articles/benchmarks_files/figure-html/unnamed-chunk-4-1.png index 78c0b610..c83b2d1b 100644 Binary files a/docs/articles/benchmarks_files/figure-html/unnamed-chunk-4-1.png and b/docs/articles/benchmarks_files/figure-html/unnamed-chunk-4-1.png differ diff --git a/docs/articles/benchmarks_files/figure-html/unnamed-chunk-6-1.png b/docs/articles/benchmarks_files/figure-html/unnamed-chunk-6-1.png index c48d8145..e5d3f4c9 100644 Binary files a/docs/articles/benchmarks_files/figure-html/unnamed-chunk-6-1.png and b/docs/articles/benchmarks_files/figure-html/unnamed-chunk-6-1.png differ diff --git a/docs/articles/index.html b/docs/articles/index.html index 77f6f0c5..a46a3176 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.1.0.9021 + 1.2.0 diff --git a/docs/articles/resistance_predict.html b/docs/articles/resistance_predict.html index 234dd590..e6db163a 100644 --- a/docs/articles/resistance_predict.html +++ b/docs/articles/resistance_predict.html @@ -39,7 +39,7 @@ AMR (for R) - 1.1.0.9021 + 1.2.0 diff --git a/docs/authors.html b/docs/authors.html index 94e69a1f..5e489fbd 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -81,7 +81,7 @@ AMR (for R) - 1.1.0.9021 + 1.2.0 diff --git a/docs/index.html b/docs/index.html index 5070eb9c..7758a052 100644 --- a/docs/index.html +++ b/docs/index.html @@ -43,7 +43,7 @@ AMR (for R) - 1.1.0.9021 + 1.2.0 diff --git a/docs/news/index.html b/docs/news/index.html index 619e5378..315a90ca 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.1.0.9021 + 1.2.0 @@ -229,14 +229,10 @@ Source: NEWS.md -
-

-AMR 1.1.0.9021 Unreleased +
+

+AMR 1.2.0 Unreleased

-
-

-Last updated: 28-May-2020 -

Breaking

@@ -296,7 +292,6 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
  • Removed function read.4d(), that was only useful for reading data from an old test database.
    • -

    diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 0ea0b550..d5269520 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -10,7 +10,7 @@ articles: WHONET: WHONET.html benchmarks: benchmarks.html resistance_predict: resistance_predict.html -last_built: 2020-05-28T08:48Z +last_built: 2020-05-28T10:26Z urls: reference: https://msberends.gitlab.io/AMR/reference article: https://msberends.gitlab.io/AMR/articles diff --git a/docs/reference/AMR-deprecated.html b/docs/reference/AMR-deprecated.html index 52cf1a2c..81947548 100644 --- a/docs/reference/AMR-deprecated.html +++ b/docs/reference/AMR-deprecated.html @@ -82,7 +82,7 @@ AMR (for R) - 1.1.0.9019 + 1.2.0

    diff --git a/docs/reference/AMR.html b/docs/reference/AMR.html index dd7cb8a3..b666f314 100644 --- a/docs/reference/AMR.html +++ b/docs/reference/AMR.html @@ -82,7 +82,7 @@ AMR (for R) - 1.1.0 + 1.2.0

    @@ -293,7 +293,7 @@ The Netherlands

    -

    Site built with pkgdown 1.5.0.

    +

    Site built with pkgdown 1.5.1.

    diff --git a/docs/reference/WHOCC.html b/docs/reference/WHOCC.html index 2812292f..2f397f2c 100644 --- a/docs/reference/WHOCC.html +++ b/docs/reference/WHOCC.html @@ -82,7 +82,7 @@ AMR (for R) - 1.1.0 + 1.2.0 @@ -272,7 +272,7 @@ This package contains all ~550 antibiotic, antimycotic and antiviral dru
    -

    Site built with pkgdown 1.5.0.

    +

    Site built with pkgdown 1.5.1.

    diff --git a/docs/reference/WHONET.html b/docs/reference/WHONET.html index 9ac0f8fd..1c678316 100644 --- a/docs/reference/WHONET.html +++ b/docs/reference/WHONET.html @@ -82,7 +82,7 @@ AMR (for R) - 1.1.0 + 1.2.0 @@ -290,7 +290,7 @@
    -

    Site built with pkgdown 1.5.0.

    +

    Site built with pkgdown 1.5.1.

    diff --git a/docs/reference/ab_property.html b/docs/reference/ab_property.html index 2c263ed7..1d598718 100644 --- a/docs/reference/ab_property.html +++ b/docs/reference/ab_property.html @@ -82,7 +82,7 @@ AMR (for R) - 1.1.0.9021 + 1.2.0 diff --git a/docs/reference/age.html b/docs/reference/age.html index 77680ac6..805ebac0 100644 --- a/docs/reference/age.html +++ b/docs/reference/age.html @@ -82,7 +82,7 @@ AMR (for R) - 1.1.0.9019 + 1.2.0 diff --git a/docs/reference/age_groups.html b/docs/reference/age_groups.html index 9c7b920a..b8efb20b 100644 --- a/docs/reference/age_groups.html +++ b/docs/reference/age_groups.html @@ -82,7 +82,7 @@ AMR (for R) - 1.1.0.9019 + 1.2.0 diff --git a/docs/reference/antibiotics.html b/docs/reference/antibiotics.html index 8e3f313c..a4dd3a17 100644 --- a/docs/reference/antibiotics.html +++ b/docs/reference/antibiotics.html @@ -82,7 +82,7 @@ AMR (for R) - 1.1.0.9004 + 1.2.0 diff --git a/docs/reference/as.ab.html b/docs/reference/as.ab.html index 4f7f03c7..566ceae5 100644 --- a/docs/reference/as.ab.html +++ b/docs/reference/as.ab.html @@ -82,7 +82,7 @@ AMR (for R) - 1.1.0.9019 + 1.2.0 diff --git a/docs/reference/as.disk.html b/docs/reference/as.disk.html index ee1d4777..ce24cf29 100644 --- a/docs/reference/as.disk.html +++ b/docs/reference/as.disk.html @@ -82,7 +82,7 @@ AMR (for R) - 1.1.0.9020 + 1.2.0 diff --git a/docs/reference/as.mic.html b/docs/reference/as.mic.html index a3f93b34..d89457ab 100644 --- a/docs/reference/as.mic.html +++ b/docs/reference/as.mic.html @@ -82,7 +82,7 @@ AMR (for R) - 1.1.0.9020 + 1.2.0 diff --git a/docs/reference/as.mo.html b/docs/reference/as.mo.html index 7e05b9d6..d845cce9 100644 --- a/docs/reference/as.mo.html +++ b/docs/reference/as.mo.html @@ -82,7 +82,7 @@ AMR (for R) - 1.1.0.9021 + 1.2.0 diff --git a/docs/reference/as.rsi.html b/docs/reference/as.rsi.html index 5a004e20..7daad110 100644 --- a/docs/reference/as.rsi.html +++ b/docs/reference/as.rsi.html @@ -82,7 +82,7 @@ AMR (for R) - 1.1.0.9020 + 1.2.0 diff --git a/docs/reference/atc_online.html b/docs/reference/atc_online.html index 198a5f7b..3d7fd6bb 100644 --- a/docs/reference/atc_online.html +++ b/docs/reference/atc_online.html @@ -83,7 +83,7 @@ This function requires an internet connection." /> AMR (for R) - 1.1.0.9019 + 1.2.0 diff --git a/docs/reference/availability.html b/docs/reference/availability.html index ffbde8be..b1ca9639 100644 --- a/docs/reference/availability.html +++ b/docs/reference/availability.html @@ -82,7 +82,7 @@ AMR (for R) - 1.1.0.9019 + 1.2.0 diff --git a/docs/reference/bug_drug_combinations.html b/docs/reference/bug_drug_combinations.html index d9f68518..fcd71754 100644 --- a/docs/reference/bug_drug_combinations.html +++ b/docs/reference/bug_drug_combinations.html @@ -82,7 +82,7 @@ AMR (for R) - 1.1.0.9019 + 1.2.0 diff --git a/docs/reference/catalogue_of_life.html b/docs/reference/catalogue_of_life.html index 5b70de3b..ed7cf2c5 100644 --- a/docs/reference/catalogue_of_life.html +++ b/docs/reference/catalogue_of_life.html @@ -82,7 +82,7 @@ AMR (for R) - 1.1.0.9021 + 1.2.0 diff --git a/docs/reference/catalogue_of_life_version.html b/docs/reference/catalogue_of_life_version.html index 5c066aee..836074f6 100644 --- a/docs/reference/catalogue_of_life_version.html +++ b/docs/reference/catalogue_of_life_version.html @@ -82,7 +82,7 @@ AMR (for R) - 1.1.0.9015 + 1.2.0 diff --git a/docs/reference/count.html b/docs/reference/count.html index c986cf79..c2ddf447 100644 --- a/docs/reference/count.html +++ b/docs/reference/count.html @@ -83,7 +83,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible( AMR (for R) - 1.1.0.9019 + 1.2.0 diff --git a/docs/reference/eucast_rules.html b/docs/reference/eucast_rules.html index a4fe41a3..66b33bf8 100644 --- a/docs/reference/eucast_rules.html +++ b/docs/reference/eucast_rules.html @@ -83,7 +83,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied AMR (for R) - 1.1.0.9019 + 1.2.0 diff --git a/docs/reference/example_isolates.html b/docs/reference/example_isolates.html index c5727c45..19c332ce 100644 --- a/docs/reference/example_isolates.html +++ b/docs/reference/example_isolates.html @@ -82,7 +82,7 @@ AMR (for R) - 1.1.0 + 1.2.0 @@ -274,7 +274,7 @@
    -

    Site built with pkgdown 1.5.0.

    +

    Site built with pkgdown 1.5.1.

    diff --git a/docs/reference/example_isolates_unclean.html b/docs/reference/example_isolates_unclean.html index 2c482a40..9f84ea4f 100644 --- a/docs/reference/example_isolates_unclean.html +++ b/docs/reference/example_isolates_unclean.html @@ -82,7 +82,7 @@ AMR (for R) - 1.1.0 + 1.2.0 @@ -269,7 +269,7 @@
    -

    Site built with pkgdown 1.5.0.

    +

    Site built with pkgdown 1.5.1.

    diff --git a/docs/reference/filter_ab_class.html b/docs/reference/filter_ab_class.html index f9437000..192b0fbd 100644 --- a/docs/reference/filter_ab_class.html +++ b/docs/reference/filter_ab_class.html @@ -82,7 +82,7 @@ AMR (for R) - 1.1.0.9019 + 1.2.0 diff --git a/docs/reference/first_isolate.html b/docs/reference/first_isolate.html index 5989e3c9..2bf68dc2 100644 --- a/docs/reference/first_isolate.html +++ b/docs/reference/first_isolate.html @@ -82,7 +82,7 @@ AMR (for R) - 1.1.0.9019 + 1.2.0 diff --git a/docs/reference/g.test.html b/docs/reference/g.test.html index 54a54887..bafe2704 100644 --- a/docs/reference/g.test.html +++ b/docs/reference/g.test.html @@ -82,7 +82,7 @@ AMR (for R) - 1.1.0.9019 + 1.2.0 diff --git a/docs/reference/ggplot_pca.html b/docs/reference/ggplot_pca.html index 2dc3a8d2..2920f01a 100644 --- a/docs/reference/ggplot_pca.html +++ b/docs/reference/ggplot_pca.html @@ -82,7 +82,7 @@ AMR (for R) - 1.1.0.9019 + 1.2.0 diff --git a/docs/reference/ggplot_rsi.html b/docs/reference/ggplot_rsi.html index e90bc0ce..e060340d 100644 --- a/docs/reference/ggplot_rsi.html +++ b/docs/reference/ggplot_rsi.html @@ -82,7 +82,7 @@ AMR (for R) - 1.1.0.9019 + 1.2.0 diff --git a/docs/reference/guess_ab_col.html b/docs/reference/guess_ab_col.html index 9ed3ecd5..ea215ecd 100644 --- a/docs/reference/guess_ab_col.html +++ b/docs/reference/guess_ab_col.html @@ -82,7 +82,7 @@ AMR (for R) - 1.1.0.9019 + 1.2.0 diff --git a/docs/reference/index.html b/docs/reference/index.html index dba6713c..2517794f 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.1.0.9021 + 1.2.0 diff --git a/docs/reference/join.html b/docs/reference/join.html index fcc9912f..f16555b5 100644 --- a/docs/reference/join.html +++ b/docs/reference/join.html @@ -82,7 +82,7 @@ AMR (for R) - 1.1.0.9019 + 1.2.0 diff --git a/docs/reference/key_antibiotics.html b/docs/reference/key_antibiotics.html index f528d663..21ef75b3 100644 --- a/docs/reference/key_antibiotics.html +++ b/docs/reference/key_antibiotics.html @@ -82,7 +82,7 @@ AMR (for R) - 1.1.0.9019 + 1.2.0 diff --git a/docs/reference/kurtosis.html b/docs/reference/kurtosis.html index da3c30fd..c963c060 100644 --- a/docs/reference/kurtosis.html +++ b/docs/reference/kurtosis.html @@ -82,7 +82,7 @@ AMR (for R) - 1.1.0.9019 + 1.2.0 diff --git a/docs/reference/lifecycle.html b/docs/reference/lifecycle.html index 170248bc..e0dd7432 100644 --- a/docs/reference/lifecycle.html +++ b/docs/reference/lifecycle.html @@ -84,7 +84,7 @@ This page contains a section for every lifecycle (with text borrowed from the af AMR (for R) - 1.1.0.9019 + 1.2.0 diff --git a/docs/reference/like.html b/docs/reference/like.html index bd040406..a04e2e5c 100644 --- a/docs/reference/like.html +++ b/docs/reference/like.html @@ -82,7 +82,7 @@ AMR (for R) - 1.1.0.9019 + 1.2.0 diff --git a/docs/reference/mdro.html b/docs/reference/mdro.html index 6f4a74d6..6763dea6 100644 --- a/docs/reference/mdro.html +++ b/docs/reference/mdro.html @@ -82,7 +82,7 @@ AMR (for R) - 1.1.0.9019 + 1.2.0 diff --git a/docs/reference/microorganisms.codes.html b/docs/reference/microorganisms.codes.html index 4dca81bf..f4ef168e 100644 --- a/docs/reference/microorganisms.codes.html +++ b/docs/reference/microorganisms.codes.html @@ -82,7 +82,7 @@ AMR (for R) - 1.1.0.9021 + 1.2.0 diff --git a/docs/reference/microorganisms.html b/docs/reference/microorganisms.html index ffe572ef..6ec1c4cf 100644 --- a/docs/reference/microorganisms.html +++ b/docs/reference/microorganisms.html @@ -82,7 +82,7 @@ AMR (for R) - 1.1.0.9021 + 1.2.0 diff --git a/docs/reference/microorganisms.old.html b/docs/reference/microorganisms.old.html index 9dbb4d48..5ef7a925 100644 --- a/docs/reference/microorganisms.old.html +++ b/docs/reference/microorganisms.old.html @@ -82,7 +82,7 @@ AMR (for R) - 1.1.0.9021 + 1.2.0 diff --git a/docs/reference/mo_property.html b/docs/reference/mo_property.html index 7a23d145..b3e0590f 100644 --- a/docs/reference/mo_property.html +++ b/docs/reference/mo_property.html @@ -82,7 +82,7 @@ AMR (for R) - 1.1.0.9021 + 1.2.0 diff --git a/docs/reference/mo_source.html b/docs/reference/mo_source.html index fa90545c..d57db017 100644 --- a/docs/reference/mo_source.html +++ b/docs/reference/mo_source.html @@ -83,7 +83,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p AMR (for R) - 1.1.0.9021 + 1.2.0 diff --git a/docs/reference/p_symbol.html b/docs/reference/p_symbol.html index 600dd4fb..e0af51cc 100644 --- a/docs/reference/p_symbol.html +++ b/docs/reference/p_symbol.html @@ -82,7 +82,7 @@ AMR (for R) - 1.1.0.9019 + 1.2.0 diff --git a/docs/reference/pca.html b/docs/reference/pca.html index 21185ca3..5981c203 100644 --- a/docs/reference/pca.html +++ b/docs/reference/pca.html @@ -82,7 +82,7 @@ AMR (for R) - 1.1.0.9019 + 1.2.0 diff --git a/docs/reference/proportion.html b/docs/reference/proportion.html index 73be35c8..6df56250 100644 --- a/docs/reference/proportion.html +++ b/docs/reference/proportion.html @@ -83,7 +83,7 @@ resistance() should be used to calculate resistance, susceptibility() should be AMR (for R) - 1.1.0.9019 + 1.2.0 diff --git a/docs/reference/resistance_predict.html b/docs/reference/resistance_predict.html index f8b4fa0b..6385724f 100644 --- a/docs/reference/resistance_predict.html +++ b/docs/reference/resistance_predict.html @@ -82,7 +82,7 @@ AMR (for R) - 1.1.0.9019 + 1.2.0 diff --git a/docs/reference/rsi_translation.html b/docs/reference/rsi_translation.html index 0c5bf48b..0e781a49 100644 --- a/docs/reference/rsi_translation.html +++ b/docs/reference/rsi_translation.html @@ -82,7 +82,7 @@ AMR (for R) - 1.1.0 + 1.2.0 @@ -277,7 +277,7 @@
    -

    Site built with pkgdown 1.5.0.

    +

    Site built with pkgdown 1.5.1.

    diff --git a/docs/reference/skewness.html b/docs/reference/skewness.html index 314dab68..8225249d 100644 --- a/docs/reference/skewness.html +++ b/docs/reference/skewness.html @@ -83,7 +83,7 @@ When negative: the left tail is longer; the mass of the distribution is concentr AMR (for R) - 1.1.0.9019 + 1.2.0 diff --git a/docs/reference/translate.html b/docs/reference/translate.html index 64921852..c23a5d7e 100644 --- a/docs/reference/translate.html +++ b/docs/reference/translate.html @@ -82,7 +82,7 @@ AMR (for R) - 1.1.0.9019 + 1.2.0